Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations
Boreogadus saida (Polar cod) is a critical ecological linkage between planktonic primary production and megafaunal top consumers in the Arctic. Despite its critical ecology, the population structure, especially the relationship between fjord and oceanic groups inhabiting environments with different...
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UiT Norges arktiske universitet
2021
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Online Access: | https://hdl.handle.net/10037/21751 |
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ftunivtroemsoe:oai:munin.uit.no:10037/21751 2023-05-15T15:00:39+02:00 Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations Hill, Griffin 2021-05-16 https://hdl.handle.net/10037/21751 eng eng UiT Norges arktiske universitet UiT The Arctic University of Norway https://hdl.handle.net/10037/21751 Copyright 2021 The Author(s) VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 full transcriptome sequencing differential gene expression BIO-3950 Master thesis Mastergradsoppgave 2021 ftunivtroemsoe 2021-07-07T22:52:38Z Boreogadus saida (Polar cod) is a critical ecological linkage between planktonic primary production and megafaunal top consumers in the Arctic. Despite its critical ecology, the population structure, especially the relationship between fjord and oceanic groups inhabiting environments with different physical characteristics, is poorly described. Though the subject of several genetic studies, an underlying biological basis for this difference is yet to be identified. Total RNA was extracted from liver tissue of 144 Polar cod representing 3 pairs of neighboring fjord and offshore populations, comprising a North-South gradient of Eastern Greenland and Svalbard. 3’ sequencing of the corresponding cDNA on two Illumina HiSeq 4000 lanes yielded approximately 14 million reads per sample upon which differential gene expression analysis was performed. After alignment and read quantification using the Atlantic Cod (Gadus morhua) genome, approximately 2,000 significantly differentially expressed (up or down regulated) genes per fjord-offshore pairing were identified. Gene ontology profiling of the differentially expressed genes by biological process revealed that distance between fjord and offshore populations is a strong predictor of gene expression between these populations. The differentially expressed biological pathways identified provide insight on the origin and structure of fjord and oceanic populations of Polar cod including evidence of gradual differentiation within the Greenland Sea based primarily on distance from the coast. This examination of a key Arctic species through the lens of a novel transcriptomic approach provides new context to previous genetic investigations as well as a unique foundational dataset for subsequent analyses of these populations. Master Thesis Arctic atlantic cod Boreogadus saida Gadus morhua Greenland Greenland Sea polar cod Svalbard University of Tromsø: Munin Open Research Archive Arctic Greenland Lanes ENVELOPE(18.933,18.933,69.617,69.617) Svalbard |
institution |
Open Polar |
collection |
University of Tromsø: Munin Open Research Archive |
op_collection_id |
ftunivtroemsoe |
language |
English |
topic |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 full transcriptome sequencing differential gene expression BIO-3950 |
spellingShingle |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 full transcriptome sequencing differential gene expression BIO-3950 Hill, Griffin Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations |
topic_facet |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 full transcriptome sequencing differential gene expression BIO-3950 |
description |
Boreogadus saida (Polar cod) is a critical ecological linkage between planktonic primary production and megafaunal top consumers in the Arctic. Despite its critical ecology, the population structure, especially the relationship between fjord and oceanic groups inhabiting environments with different physical characteristics, is poorly described. Though the subject of several genetic studies, an underlying biological basis for this difference is yet to be identified. Total RNA was extracted from liver tissue of 144 Polar cod representing 3 pairs of neighboring fjord and offshore populations, comprising a North-South gradient of Eastern Greenland and Svalbard. 3’ sequencing of the corresponding cDNA on two Illumina HiSeq 4000 lanes yielded approximately 14 million reads per sample upon which differential gene expression analysis was performed. After alignment and read quantification using the Atlantic Cod (Gadus morhua) genome, approximately 2,000 significantly differentially expressed (up or down regulated) genes per fjord-offshore pairing were identified. Gene ontology profiling of the differentially expressed genes by biological process revealed that distance between fjord and offshore populations is a strong predictor of gene expression between these populations. The differentially expressed biological pathways identified provide insight on the origin and structure of fjord and oceanic populations of Polar cod including evidence of gradual differentiation within the Greenland Sea based primarily on distance from the coast. This examination of a key Arctic species through the lens of a novel transcriptomic approach provides new context to previous genetic investigations as well as a unique foundational dataset for subsequent analyses of these populations. |
format |
Master Thesis |
author |
Hill, Griffin |
author_facet |
Hill, Griffin |
author_sort |
Hill, Griffin |
title |
Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations |
title_short |
Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations |
title_full |
Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations |
title_fullStr |
Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations |
title_full_unstemmed |
Transcriptomic basis for differentiation of fjord and offshore Boreogadus saida (Polar cod) populations |
title_sort |
transcriptomic basis for differentiation of fjord and offshore boreogadus saida (polar cod) populations |
publisher |
UiT Norges arktiske universitet |
publishDate |
2021 |
url |
https://hdl.handle.net/10037/21751 |
long_lat |
ENVELOPE(18.933,18.933,69.617,69.617) |
geographic |
Arctic Greenland Lanes Svalbard |
geographic_facet |
Arctic Greenland Lanes Svalbard |
genre |
Arctic atlantic cod Boreogadus saida Gadus morhua Greenland Greenland Sea polar cod Svalbard |
genre_facet |
Arctic atlantic cod Boreogadus saida Gadus morhua Greenland Greenland Sea polar cod Svalbard |
op_relation |
https://hdl.handle.net/10037/21751 |
op_rights |
Copyright 2021 The Author(s) |
_version_ |
1766332728042586112 |